ArticleBioinformatics (Oxford, England)2012
Hybrid spatial Gillespie and particle tracking simulation.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 36 citations in OpenAlex.
- The blending region hybrid framework for the simulation of stochastic reaction-diffusion processes.Journal of the Royal Society, Interface · 2020Article
- Stochastic self-tuning hybrid algorithm for reaction-diffusion systems.The Journal of chemical physics · 2019Article
- Potential based, spatial simulation of dynamically nested particles.BMC bioinformatics · 2019Article
- Multiscale Stochastic Reaction-Diffusion Algorithms Combining Markov Chain Models with Stochastic Partial Differential Equations.Bulletin of mathematical biology · 2019Article
- Spatially extended hybrid methods: a review.Journal of the Royal Society, Interface · 2018Review
- Coupling volume-excluding compartment-based models of diffusion at different scales: Voronoi and pseudo-compartment approaches.Journal of the Royal Society, Interface · 2016Article
- Multiscale reaction-diffusion simulations with Smoldyn.Bioinformatics (Oxford, England) · 2015Article
- Convergence of methods for coupling of microscopic and mesoscopic reaction-diffusion simulations.Journal of computational physics · 2015Article
- The pseudo-compartment method for coupling partial differential equation and compartment-based models of diffusion.Journal of the Royal Society, Interface · 2015Article
- Stochastic reaction-diffusion processes with embedded lower-dimensional structures.Bulletin of mathematical biology · 2014Article
- Single molecule simulations in complex geometries with embedded dynamic one-dimensional structures.The Journal of chemical physics · 2013Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationCellular signal transduction involves spatial-temporal dynamics and often stochastic effects due to the low particle abundance of some molecular species. Others can, however, be of high abundances. Such a system can be simulated either with the spatial Gillespie/Stochastic Simulation Algorithm (SSA) or Brownian/Smoluchowski dynamics if space and stochasticity are important. To combine the accuracy of particle-based methods with the superior performance of the SSA, we suggest a hybrid simulation.
resultsThe proposed simulation allows an interactive or automated switching for regions or species of interest in the cell. Especially we see an application if for instance receptor clustering at the membrane is modeled in detail and the transport through the cytoplasm is included as well. The results show the increase in performance of the overall simulation, and the limits of the approach if crowding is included. Future work will include the development of a GUI to improve control of the simulation. AVAILABILITY OF IMPLEMENTATION: www.bison.ethz.ch/research/spatial_simulations. CONTACT: mklann@ee.ethz.ch or koeppl@ethz.ch Supplementary/Information: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.